Free-energy calculations - Theoretical Biophysics Group

(a) 2.4
P(∆U )
2.0
1.6
1.2
0.8
P 1 (∆U )
0.4
1
0.0
-1.2 -0.8 -0.4 0 0.4 0.8 1.2 1.6
(b) 2.4
∆U
P(∆U )
2.0
1.6
1.2
0.8
0.4
P 1 (∆U )
Free-energy perturbation calculations A pictorial representation of free-energy perturbation
P 0 (∆U )
P 0 (∆U )
0.0
-1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6
∆U
(c) 2.4
P(∆U )
2.0
1.6
1.2
P 1 (∆U )
0.8
no sampling
0.4
P 0 (∆U )
0.0
-1 -0.8 -0.6 -0.4 -0.2 0
∆U
(d) 2.4
0
0.2 0.4 0.6
2.0 i
P (∆U ) 1
1.6
1.2
1
P (∆U )
0
P(∆U )
0.8
1
1
0
0
0.4
P(∆U )
i,i+1
0.0
-1.2 -0.8 -0.4 0
∆U
0.4 0.8 1.2
18 LU, KOFKE (2001)
0
A pictorial representation of the relationship between the reference
and the target systems may constitute a useful tool to detect
inaccuracies caused by incomplete sampling. 18
If the important region of the target system fully overlaps, or is a
subset of the important region of the reference system, P0(∆U)
estimated from FEP calculations should be reliable.
Good sampling of the important region in the reference system
will also yield good sampling of the important region in the target
system.
If the important regions of the two systems do not overlap, the important
region of the target state is not expected to be sufficiently
sampled during a simulation of the reference system. Satisfactory
estimates of ∆A are unlikely to be obtained.
Chris Chipot Free-energy calculations